Accurate adsorption energies for small molecules on oxide surfaces: CH4/MgO(001) and C2H6/MgO(001)

A hybrid method is applied that combines second order Møller–Plesset perturbation theory (MP2) for cluster models with density functional theory for periodic (slab) models to obtain structures and energies for methane and ethane molecules adsorbed on the MgO(001) surface. Single point calculations are performed to estimate the effect of increasing the cluster size on the MP2 energies and to evaluate the difference between coupled cluster (CCSD(T)) and MP2 energies. The final estimates of the adsorption energies are 12.9 ± 1.3 and 18.9 ± 1.8 kJ/mol for CH₄ and C₂H₆, respectively. © 2016 Wiley Periodicals, Inc.     

Theoretical determination of lowest structures of all‐metal aromatic clusters M4L2 (M = Al,Ga, In,Tl; L = Li,Na, K,Rb, Cs)

The researches of all‐metal aromatic clusters have been a thermic theme in inorganic aromaticity domain both experimentally and theoretically since the Al₄L^? (L = Li, Na, Cu) clusters were created by laser vaporization. In systemic determination of the lowest structures of 20 gaseous all‐metal aromatic clusters M₄L₂ (M = Al, Ga, In, Tl; L = Li, Na, K, Rb, Cs), the isomer energy differences of four low‐lying structures of each cluster were evaluated at high‐quality quantum chemistry levels. Single point calculations at the coupled cluster level were performed at geometries optimized at the MP2, B3LYP, and B3PW91 levels, and harmonic frequency calculations and zero point energy corrections were implemented following optimizations at the B3LYP and B3PW91 levels. In addition to Li‐ and Na‐containing species, theoretical investigations came down to those new clusters including K, Rb, and Cs. For many clusters, the most convincing theoretical evidences indicate that the lowest structures are a square bipyramidal isomer rather than an edge‐caped square pyramidal species. A few discrepancies were addressed at the MP2, B3LYP, and B3PW91 levels in comparison with the coupled cluster results. These findings are significant because some clusters were generated by laser vaporization and served as theoretical prototypes to test the new means for assessing aromaticity. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Structure and stability of B8 clusters

We investigated various isomers of B₈ clusters with ab initio (MP2) and density function theory (DFT) methods (B3LYP and B3PW91). Nineteen B₈ isomers were determined to be local minima on their potential energy hypersurfaces by the B3LYP, B3PW91, and MP2 methods. Fifteen of these structures are first reported. The most stable neutral B₈ cluster is the regular heptagon, with another boron atom at the center (D_7h, triplet), in agreement with results reported previously. The natural bond orbital (NBO) analysis and nucleus‐independent chemical shifts (NICS) further reveal that the most stable species have delocalized π bond and multicentered σ bonds and therefore exhibit multiple‐fold aromaticity. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.     

Quantum mechanics investigation on initial decomposition of ammonia borane in glyme

The chemical kinetics of ammonia borane (AB) in glyme solution is studied using quantum mechanics (QM) based calculations along with experimental results available in the literature. The primary objective of this study is to propose a detailed reaction mechanism that explains the formation of species observed during AB decomposition for temperatures ranging from 323 to 368 K. The quantum mechanics investigation uses transition state theory to identify the relevant reaction pathways. Intrinsic reaction coordinate calculations use the identified transition‐state structure to link the reactants to the products. These calculations were performed using the Gaussian 09 program package, including the solvation model based on density (SMD) with acetonitrile as the solvent. Thermodynamic properties of species at equilibrium or at transition states were computed using the G4(MP2) compound method. Sensitivity analysis was performed using a species conservation model to identify reactions and species that play a critical role. This study confirms the previous experimental observation regarding the initiation of decomposition of AB in glyme. It also elucidates the role of DADB, ammonium borohydride salt ([BH₄]⁻[NH₄]⁺) and BH₂NH₂ in hydrogen release and intermediates formed during initial phase of AB decomposition. This work shows how QM calculations along with experimental results can contribute to our understanding of the complex chemical kinetics involved during AB dehydrogenation.     

CPMD/GULP QM/MM interface for modeling periodic solids: Implementation and its application in the study of Y‐zeolite supported Rhn clusters

We report here the development of hybrid quantum mechanics/molecular mechanics (QM/MM) interface between the plane‐wave density functional theory based CPMD code and the empirical force‐field based GULP code for modeling periodic solids and surfaces. The hybrid QM/MM interface is based on the electrostatic coupling between QM and MM regions. The interface is designed for carrying out full relaxation of all the QM and MM atoms during geometry optimizations and molecular dynamics simulations, including the boundary atoms. Both Born–Oppenheimer and Car–Parrinello molecular dynamics schemes are enabled for the QM part during the QM/MM calculations. This interface has the advantage of parallelization of both the programs such that the QM and MM force evaluations can be carried out in parallel to model large systems. The interface program is first validated for total energy conservation and parallel scaling performance is benchmarked. Oxygen vacancy in α‐cristobalite is then studied in detail and the results are compared with a fully QM calculation and experimental data. Subsequently, we use our implementation to investigate the structure of rhodium cluster (Rh_n; n = 2 to 6) formed from Rh(C₂H₄)₂ complex adsorbed within a cavity of Y‐zeolite in a reducible atmosphere of H₂ gas. © 2016 Wiley Periodicals, Inc.     

Ab initio calculations and molecular dynamics simulation of H2 adsorption on CN3Be3+ cluster

Hydrogen adsorption properties of the CN₃Be₃⁺ cluster have been studied using density functional theory and MP2 method with a 6–31++G** basis set. Five hydrogen molecules get adsorbed on the CN₃Be₃⁺ cluster with a hydrogen storage capacity of 10.98 wt%. Adsorption of three H₂ molecules on one of the three Be atoms in a cluster is reported for the first time. It is due to the more positive charge on this Be atom than the remaining two. The average value for H₂ adsorption energy in CN₃Be₃⁺ (5H₂) complexes is 0.41 (0.43) eV/H₂ at MP2 (wB97XD) level, which fits well within the ideal range. Adsorption energy from electronic structure calculations plays an important role in retaining the number of H₂ molecules on a cluster during atom-centered density matrix propagation (ADMP) molecular dynamics (MD) simulations. According to ADMP-MD simulations, out of five H₂ adsorbed molecules on CN₃Be₃⁺, four and two H₂ molecules remain absorbed on CN₃Be₃⁺ cluster at 275 K and 350 K, respectively, during the simulation.

     

Au10团簇结构与电性质的理论研究

使用4种流行的泛函(BPW91, B3PW91, PW91和B3LYP)考查了若干Au10团簇结构的稳定结构, 获得了能量最有利的6种异构体(其中2种以前未见报道), 并在此基础上进一步用MP2方法校准了它们的相对稳定性, 分析了它们的电子性质以及最稳定异构体与氧分子的化学反应性能. 计算结果表明Au10团簇异构体的相对稳定性明显依赖所使用的理论方法和泛函, 密度泛函结果显示Au10倾向于采用平面结构, 且不同的泛函给出异构体的相对稳定性次序也不相同, 而MP2计算则显示三维空间结构的Au10团簇更稳定, Au10可能是金团簇从二维结构到三维结构演化的一个临界点.     

Structures and stability of N9, N9 − and N9 + clusters

 Ab initio molecular orbital calculations for N₉, N⁻ ₉ and N⁺ ₉ isomers were carried out at the HF/ 6-31G*, B3PW91/6-31G*, B3LYP/6-31G* and MP2/ 6-31G* levels of theory. Stable equilibrium geometric structures were determined by harmonic vibrational frequency analyses at the HF/6-31G*, B3PW91/6-31G* and B3LYP/6-31G* levels of theory. The most stable free-radical N₉ cluster is structure 1 with C _{2 v} symmetry and that of anion N⁻ ₉ is structure 3 with C _s symmetry. Only one stable structure of the N⁺ ₉ cation with C _{2 v} symmetry was predicted. Their potential application as high-energy-density materials has been examined. Received: 15 June 1999 / Accepted: 11 October 1999 / Published online: 14 March 2000     

Theoretical studies of the gas‐phase pyrolysis kinetics of ω‐bromonitriles,ZCH2CH2Br [Z = NC,NCCH2, NCCH2CH2]

The gas‐phase elimination of several ω‐bromonitriles (ZCH₂CH₂Br, Z = NC, NCCH₂, NCCH₂CH₂) has been examined at the MP2/6‐31G(d,p), MP2/6‐31G(2d,2p), B3PW91/6‐31G(2d,2p), and MPW91PW91/6‐31(2p,2d) levels of theory. The bromonitriles yield the corresponding cyano‐olefin and HBr gas in a rate‐determining step. The MPW91PW91/6‐31G(2p,2d) results suggest a concerted mechanism, with a polar, four‐membered transition state. The calculated kinetic and thermodynamic parameters were found to be within reasonable agreement with the experimental determinations. Substituent effects are discussed in terms of electronic structure. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 41: 168–175, 2009     

Verification of DFT-predicted hydrogen storage capacity of VC3H3 complex using molecular dynamics simulations

Density functional theory (DFT) and Fourth‐order Möller–Plesset (MP4) perturbation theory calculations are performed to examine the possibility of hydrogen storage in V‐capped VC₃H₃ complex. Stability of bare and H₂ molecules adsorbed V‐capped VC₃H₃ complex is verified using DFT and MP4 method. Thermo‐chemistry calculations are carried out to estimate the Gibbs free corrected averaged H₂ adsorption energy which reveals whether H₂ adsorption on V‐capped VC₃H₃ complex is energetically favorable, at different temperatures. We use different exchange and correlation functionals employed in DFT to see their effect on H₂ adsorption energy. Molecular dynamic (MD) simulations are performed to confirm whether this complex adsorbs H₂ molecules at a finite temperature. We elucidate the correlation between H₂ adsorption energy obtained from density functional calculations and retaining number of H₂ molecules on VC₃H₃ complex during MDs simulations at various temperatures. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

DFT studies of the phosphinidene derivative HPNaF and its insertion reaction with R–H(R=F,OH, NH<Subscript>2</Subscript>, CH<Subscript>3</Subscript>)

The formations of the phosphinidene derivative HPNaF and its insertion reactions with R–H (R=F, OH, NH₂, CH₃) have been systematically investigated employing the density functional theory (DFT), such as the B3LYP and MPW1PW91 methods. A comparison with the results of MP2 calculations shows that MPW1PW91 underestimates the barrier heights for the four reactions considered. Similarly, the same is also true for the B3LYP method depending on the selected reactions, but by much less than MPW1PW91, where the barrier heights of the four reactions are 25.2, 85.7, 119.0, and 142.4 kJ/mol at the B3LYP/6-311+G* level of theory, respectively. All the mechanisms of the four reactions are identical to each other, i.e., an intermediate has been located during the insertion reaction. Then, the intermediate could dissociate to substituted phosphinidane(H₂RP) and NaF with a barrier corresponding to their respective dissociation energies. Correspondingly, the reaction energies for the four reactions are −92.2, −68.1, −57.2, and −44.3 kJ/mol at the B3LYP/6-311+G* level of theory, respectively, where both the B3LYP and MPW1PW91 methods underestimate the reaction energies compared with the MP2 results. The linear correlations between the calculated barrier heights and the reaction energies have also been observed. As a result, the relative reactivity among the four insertion reactions should be as follows: H–F > H–OH > H–NH₂ > H–CH₃.     

An embedded QM/MM study for different SiO2/Al2O3 ratios of the HZSM‐5 zeolite and for their interaction with n‐heptane

We carried out a theoretical study of the HZSM‐5 zeolite, for different SiO₂/Al₂O₃ ratios, that interacts with the n‐heptane molecule. The study was performed using a QM/MM (quantum mechanics/molecular mechanics) methodology. For the QM part, we have chosen a hybrid Hartree‐Fock density functional theory (DFT). The hybrid ACM/DZP approach, as implemented in Turbomole, was used for the treatment of the QM cluster containing 84 atoms that represents a ring structure model of the zeolite‐n‐heptane interacting system. The MM part was represented by means of an electrostatic forcefield (ESFF), which assesses the electronic embedding. The chosen QM/MM silicalite base model contains 3862 atoms. The studied SiO₂/Al₂O₃ ratios were 2300, 573.5, 287.7, and 189.83, containing 1, 4, 8, and 12 Al atoms, respectively. For the first ratio, the site for the substitution of Al for Si was that of minimum QM total energy value, because this replacement was done in the QM region. For the other SiO₂/Al₂O₃ ratios, the Al atoms were randomly spread through the MM region in accordance with the Lowenstein substitution rule. These results show the importance of the environment on the electronic properties in the QM region, where the active site lies, and their effects on the earlier steps on the activation experienced by the n‐heptane moiety. A minimal content of 12 Al atoms produces significant effects of the environment on the electronic structure of the QM region. Moreover, the carbocationic character of n‐heptane increases with the aluminum content. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Intermolecular potentials of the silane dimer calculated with Hartree-Fock theory, Møller-Plesset perturbation theory, and density functional theory

We have calculated the intermolecular interaction potentials of the silane dimer at the D3d conformation using the Hartree-Fock (HF) self-consistent theory, the correlation-corrected second-order M?ller-Plesset (MP2) perturbation theory, and the density functional theory (DFT) with 108 functionals chosen from the combinations of 9 exchange and 12 correlation functionals. Single-point coupled cluster [CCSD(T)] calculations have also been carried out to calibrate the correlation effect. The HF calculations yield unbound potentials largely because of the exchange-repulsion interaction. In the MP2 calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater type orbitals fitted with Gaussian functions (STO-nG, n = 3 approximately 6), Pople's medium size basis sets [up to 6-311++G(3df,3pd)], to Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(3d,3p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy ( approximately 0.05 kcal/mol). Up to the largest basis set used, the asymptotic dispersion coefficient has not converged to the expected C6 value from molecular polarizability calculations. We attribute the slow convergence partly to the inefficacy of using the MP2 calculations with Gaussian type functions to model the asymptotic behavior. Both the basis set superposition error (BSSE) corrected and uncorrected results are presented to emphasize the importance of including such corrections. Only the BSSE corrected results systematically converge to the expected potential curve with increasing basis size. The DFT calculations generate a wide range of interaction patterns, from purely unbound to strongly bound, underestimating or overestimating the binding energy. The binding energies calculated using the OPTXHCTH147, PBEVP86, PBEP86, PW91TPSS, PW91PBE, and PW91PW91 functionals and the equilibrium bond lengths calculated using the MPWHCTH93, TPSSHCTH, PBEVP86, PBEP86, PW91TPSS, PW91PBE, and PW91PW91 functionals are close to the MP2 results using the 6-311++G(3df,3pd) basis set. A correlation between the calculated DFT potentials and the exchange and correlation enhancement factors at the low-density region has been elucidated. The asymptotic behaviors of the DFT potentials are also analyzed.     

CH3S自由基H迁移异构化及脱H2反应的直接动力学研究

采用密度泛函方法(MPW1PW91)在6-311G(d,p)基组水平上研究了CH₃S自由基H迁移反应CH₃S→CH₂SH (R1), 脱H₂反应CH₃S→HCS＋H₂ (R2)以及脱H₂产物HCS异构化反应HCS→CSH (R3)的微观动力学机理. 在QCISD(t)/6- 311＋＋G(d,p)//MPW1PW91/6-311G(d,p)＋ZPE水平上进行了单点能校正. 利用经典过渡态理论(TST)与变分过渡态理论(CVT)分别计算了各反应在200～2000 K温度区间内的速率常数k^TST和k^CVT, 同时获得了经小曲率隧道效应模型(SCT)校正后的速率常数k^CVT/SCT. 结果表明, 反应 R1, R2 和R3的势垒△E^≠分别为160.69, 266.61和241.63 kJ/mol, R1为反应的主通道. 低温下CH₃S比CH₂SH稳定, 高温时CH₂SH比CH₃S更稳定. 另外, 速率常数计算结果显示, 量子力学隧道效应在低温段对速率常数的计算有显著影响, 而变分效应在计算温度段内对速率常数的影响可以忽略.     

Water solvent effects using continuum and discrete models: The nitromethane molecule,CH3NO2

The first three valence transitions of the two nitromethane conformers (CH₃NO₂) are two dark n → π* transitions and a very intense π → π* transition. In this work, these transitions in gas‐phase and solvated in water of both conformers were investigated theoretically. The polarizable continuum model (PCM), two conductor‐like screening (COSMO) models, and the discrete sequential quantum mechanics/molecular mechanics (S‐QM/MM) method were used to describe the solvation effect on the electronic spectra. Time dependent density functional theory (TDDFT), configuration interaction including all single substitutions and perturbed double excitations (CIS(D)), the symmetry‐adapted‐cluster CI (SAC‐CI), the multistate complete active space second order perturbation theory (CASPT2), and the algebraic‐diagrammatic construction (ADC(2)) electronic structure methods were used. Gas‐phase CASPT2, SAC‐CI, and ADC(2) results are in very good agreement with published experimental and theoretical spectra. Among the continuum models, PCM combined either with CASPT2, SAC‐CI, or B3LYP provided good agreement with available experimental data. COSMO combined with ADC(2) described the overall trends of the transition energy shifts. The effect of increasing the number of explicit water molecules in the S‐QM/MM approach was discussed and the formation of hydrogen bonds was clearly established. By including explicitly 24 water molecules corresponding to the complete first solvation shell in the S‐QM/MM approach, the ADC(2) method gives more accurate results as compared to the TDDFT approach and with similar computational demands. The ADC(2) with S‐QM/MM model is, therefore, the best compromise for accurate solvent calculations in a polar environment. © 2015 Wiley Periodicals, Inc.     

Development of a 3-body:many-body integrated fragmentation method for weakly bound clusters and application to water clusters (H2O)(n = 3-10, 16, 17)

A 3-body:many-body integrated quantum mechanical (QM) fragmentation method for non-covalent clusters is introduced within the ONIOM formalism. The technique captures all 1-, 2-, and 3-body interactions with a high-level electronic structure method, while a less demanding low-level method is employed to recover 4-body and higher-order interactions. When systematically applied to 40 low-lying (H(2)O)(n) isomers ranging in size from n = 3 to 10, the CCSD(T):MP2 3-body:many-body fragmentation scheme deviates from the full CCSD(T) interaction energy by no more than 0.07 kcal mol(-1) (or <0.01 kcal mol(-1) per water). The errors for this QM:QM method increase only slightly for various low-lying isomers of (H(2)O)(16) and (H(2)O)(17) (always within 0.13 kcal mol(-1) of the recently reported canonical CCSD(T)/aug-cc-pVTZ energies). The 3-body:many-body CCSD(T):MP2 procedure is also very efficient because the CCSD(T) computations only need to be performed on subsets of the cluster containing 1, 2, or 3 monomers, which in the current context means the largest CCSD(T) calculations are for 3 water molecules, regardless of the cluster size.     

De novo prediction of the ground state structure of transition metal complexes using semiempirical and ab initio quantum mechanics. Coordination isomerism

The ground state coordination isomers for 30 different trigonal bipyramidal transition metal complexes have been predicted using different levels of quantum mechanics: semiempirical (PM3(tm)), ab initio (MP2//HF), pure (BPW91) and hybrid (B3PW91) density functional theory (DFT) methods. For species where these methods failed to reproduce crystallographic data, hybrid quantum mechanics/molecular mechanics (QM/MM) methods were used to study more exact experimental models. Literature deficiencies regarding ground state multiplicity of these species were supplemented by spin predictions using previously tested PM3(tm) methods. Geometry optimization calculations were performed for each possible coordination isomer. The predicted ground state minima provided by the different methods are compared to each other and with crystallographic data. Pure DFT functionals outperformed hybrid functionals and MP2//HF. The very rapid PM3(tm) parameterization method provided accurate predictions in comparison to other levels of theory. An integrated MM/PM3(tm)/DFT de novo scheme accurately reproduced crystallographic data for species where the individual methods failed.     

Reaction mechanism of HSH and CH3SH with NH2CH2COCH2X (X = F and Cl) molecules

The reaction mechanism of model compounds H₂S and CH₃SH for cysteine proteases with NH₂CH₂COCH₂X (X = F and Cl) molecules has been investigated using DFT methods with B3LYP and B3PW91 hybrid density functionals at 6‐31+G* basis sets. The single point energy has been calculated for the above reactions with B3LYP and B3PW91 functionals using aug‐cc‐PVDZ infinite basis set in both gas and solution phases. The intrinsic reaction coordinates calculations have been performed to confirm that each transition state is linked by the desired reactants and products. The geometries and relative energies for various stationary points have been determined and discussed. The zero point vibrational energy corrections have been made to predict the reliable energy. The negative value of reaction energy indicates that the overall reaction profile is found to be exothermic. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008